# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.unmapped.bam
# seq_deb : GTGATAGTC
# seq_fin : TCTCT
# MS_seq : A
# excl : C,G,T
# nom  : A20
# =============================
#
#-------------- Filt ------------------
# condiGrep: GTGA.AGTC[ATCGN]+AAAAA[ATCGN]+.CTCT|GTGA.AGTC[ATCGN]+AAAAA[ATCGN]+T.TCT|GTGA.AGTC[ATCGN]+AAAAA[ATCGN]+TC.CT|GTGA.AGTC[ATCGN]+AAAAA[ATCGN]+TCT.T|GTGA.AGTC[ATCGN]+AAAAA[ATCGN]+TCTC.|GTGAT.GTC[ATCGN]+AAAAA[ATCGN]+.CTCT|GTGAT.GTC[ATCGN]+AAAAA[ATCGN]+T.TCT|GTGAT.GTC[ATCGN]+AAAAA[ATCGN]+TC.CT|GTGAT.GTC[ATCGN]+AAAAA[ATCGN]+TCT.T|GTGAT.GTC[ATCGN]+AAAAA[ATCGN]+TCTC.|GTGATA.TC[ATCGN]+AAAAA[ATCGN]+.CTCT|GTGATA.TC[ATCGN]+AAAAA[ATCGN]+T.TCT|GTGATA.TC[ATCGN]+AAAAA[ATCGN]+TC.CT|GTGATA.TC[ATCGN]+AAAAA[ATCGN]+TCT.T|GTGATA.TC[ATCGN]+AAAAA[ATCGN]+TCTC.|GTGATAG.C[ATCGN]+AAAAA[ATCGN]+.CTCT|GTGATAG.C[ATCGN]+AAAAA[ATCGN]+T.TCT|GTGATAG.C[ATCGN]+AAAAA[ATCGN]+TC.CT|GTGATAG.C[ATCGN]+AAAAA[ATCGN]+TCT.T|GTGATAG.C[ATCGN]+AAAAA[ATCGN]+TCTC.|GTGATAGT.[ATCGN]+AAAAA[ATCGN]+.CTCT|GTGATAGT.[ATCGN]+AAAAA[ATCGN]+T.TCT|GTGATAGT.[ATCGN]+AAAAA[ATCGN]+TC.CT|GTGATAGT.[ATCGN]+AAAAA[ATCGN]+TCT.T|GTGATAGT.[ATCGN]+AAAAA[ATCGN]+TCTC.
# condiGrep Rev-Compt: .GAGA[NCGAT]+TTTTT[NCGAT]+.ACTATCAC|A.AGA[NCGAT]+TTTTT[NCGAT]+.ACTATCAC|AG.GA[NCGAT]+TTTTT[NCGAT]+.ACTATCAC|AGA.A[NCGAT]+TTTTT[NCGAT]+.ACTATCAC|AGAG.[NCGAT]+TTTTT[NCGAT]+.ACTATCAC|.GAGA[NCGAT]+TTTTT[NCGAT]+G.CTATCAC|A.AGA[NCGAT]+TTTTT[NCGAT]+G.CTATCAC|AG.GA[NCGAT]+TTTTT[NCGAT]+G.CTATCAC|AGA.A[NCGAT]+TTTTT[NCGAT]+G.CTATCAC|AGAG.[NCGAT]+TTTTT[NCGAT]+G.CTATCAC|.GAGA[NCGAT]+TTTTT[NCGAT]+GA.TATCAC|A.AGA[NCGAT]+TTTTT[NCGAT]+GA.TATCAC|AG.GA[NCGAT]+TTTTT[NCGAT]+GA.TATCAC|AGA.A[NCGAT]+TTTTT[NCGAT]+GA.TATCAC|AGAG.[NCGAT]+TTTTT[NCGAT]+GA.TATCAC|.GAGA[NCGAT]+TTTTT[NCGAT]+GAC.ATCAC|A.AGA[NCGAT]+TTTTT[NCGAT]+GAC.ATCAC|AG.GA[NCGAT]+TTTTT[NCGAT]+GAC.ATCAC|AGA.A[NCGAT]+TTTTT[NCGAT]+GAC.ATCAC|AGAG.[NCGAT]+TTTTT[NCGAT]+GAC.ATCAC|.GAGA[NCGAT]+TTTTT[NCGAT]+GACT.TCAC|A.AGA[NCGAT]+TTTTT[NCGAT]+GACT.TCAC|AG.GA[NCGAT]+TTTTT[NCGAT]+GACT.TCAC|AGA.A[NCGAT]+TTTTT[NCGAT]+GACT.TCAC|AGAG.[NCGAT]+TTTTT[NCGAT]+GACT.TCAC
#--------------------------------------
module load picard/2.8.2
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar SortSam I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.unmapped.sam O=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.unmapped.sort.sam SORT_ORDER=queryname 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/10-N3-12cycles-IDT.A20.unmapped.bam ]
